User: aih5

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aih50
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Posts by aih5

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Problems in identifying heterozygous transcripts using de novo transcriptome assembly via Trinity (galaxy)
... Hello, I have been annotating a genomic region that is heterozygous in our model animal. There are 10 genes I'm interested in and they all have 2 distinct alleles (sequences are not identical, 30-300 nucleotide differences over ~1000-1500 bases). We have assembled a transcriptome and aligned it to t ...
assembly rna-seq transcriptome written 2.4 years ago by aih50 • updated 2.3 years ago by Biostar ♦♦ 20
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Comment: C: How does HISAT calculate the alignment score? (and other TopHat to HISAT questio
... In response to question 1, what do the parameters -I and -X (min and max fragment length) have to do with the paired end parameters. I guess I don't completely understand the correlation between these and the other parameters such as disabling looking for discordant mates, etc. ...
written 3.0 years ago by aih50
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How does HISAT calculate the alignment score? (and other TopHat to HISAT questions)
... I've recently switched from using TopHat to using HISAT. Trying to figure out which parameters do what I want has been a bit of a challenge in spite of the manual. I realize some things may not be explainable as they are proprietary. But I think a few of my questions can be addressed. > 1. Is th ...
alignment rna-seq written 3.0 years ago by aih50 • updated 2.5 years ago by ataulhaleem0

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